Bolivia reacted with fury after a plane carrying the country's president home from Russia was diverted to Vienna amid suspicions that it was carrying the surveillance whistleblower, Edward Snowden.

France and Portugal were accused of withdrawing permission for the plane, carrying the president, Evo Morales, from energy talks in Moscow, to pass through their airspace.

Officials in both Austria and Bolivia said Snowden was not on the plane. The Bolivian foreign minister, David Choquehuanca, said: "We don't know who invented this lie. We want to denounce to the international community this injustice with the plane of President Evo Morales."

In a midnight press conference, Bolivian vice-president Alvaro Garcia said Italy and Spain had also denied the plane permission to fly through their airspace. He described Morales as being "kidnapped by imperialism" in Europe.

"The ambassador for Spain in Austria has just informed us that there is no authorisation to fly over Spanish territory and that at 9am Wednesday they would be in contact with us again," defence minister Ruben Saavedra said. The Spanish government had made "revision of the presidential plane" a condition of granting it passage, he said.

Saavedra, who was on the flight, said: "This is a hostile act by the United States state department which has used various European governments."

Morales finally left Vienna at around 11.30am local time on Wednesday, after spending 12 hours at the airport.

Choquehuanca earlier told reporters in Bolivia that Portugal and France had abruptly cancelled air permits. "They say it was due to technical issues, but after getting explanations from some authorities we found that there appeared to be some unfounded suspicions that Mr Snowden was on the plane."

He said Spain's government allowed the plane to be refuelled in its territory. From there the plane flew on to Vienna. Choquehuanca said the decision by France and Portugal "put at risk the life of the president".

The White House said the issue was a matter for European authorities and declined to comment further.

Officials at Portugal's foreign ministry and National Civil Aviation Authority could not be reached for comment. French government officials reached overnight said they could not confirm whether Morales' plane was denied permission to fly over France.

The precautions may have been prompted by a desire among governments in Paris and Lisbon to avoid entanglement in the affair – especially with public opinion in Europe running strongly against revelations of US spying.

The Austrian president, Heinz Fischer, visited Morales at the airport in the early hours of Wednesday and later said that the plane had been cleared to leave. "The flight route is normal, as far as I am informed. Spain's airspace is also open for him. [Morales] will resume his trip shortly," he said.

Fischer said that he made the visit to make sure that "our procedures here in Vienna were all correct". He told state radtio that the pair also discussed other matters.

As other options began to fade for Snowden, trapped in the transit zone of a Moscow airport, Morales said his country was keen to "shield the denounced".

Morales said Bolivia had not received a formal application for asylum from Snowden yet, but hinted it would consider any request favourably.

"If there were a request, of course we would be willing to debate and consider the idea," Morales told RT Actualidad, the Spanish-language service of Russian broadcaster RT.

"I know that the empires have an espionage network and are against the so-called developing countries. And in particular, against those which are rich in natural resources," he added.

His comments were echoed by favourable noises from Venezuela, another possible exit route for the former NSA contractor. President Nicolás Maduro said Caracas was also ready to consider Snowden's asylum should he ask for it.

Maduro said Snowden should be given a "humanitarian medal" for revealing details of NSA surveillance programmes on US and foreign citizens. "He did not kill anyone and did not plant a bomb," Maduro told Russia's Interfax news agency. "What he did was tell a great truth in an effort to prevent wars. He deserves protection under international and humanitarian law."

Snowden's father, meanwhile, stepped up the rhetoric in favour of his son's actions on Tuesday, publishing an open letter that compared him to colonial independence fighter Paul Revere. The letter was signed by Lon Snowden and his lawyer, Bruce Fein, who also reported receiving a phone call from WikiLeaks founder Julian Assange. Fein told the Associated Press that Assange, in the phone call on Saturday, delivered what he said was a message from Snowden to his father, asking him to keep quiet.

In the open letter, Lon Snowden wrote in glowing terms about his son.

"You have forced onto the national agenda the question of whether the American people prefer the right to be left alone from government snooping absent probable cause to believe crime is afoot to vassalage," he wrote. "You are a modern day Paul Revere: summoning the American people to confront the growing danger of tyranny and one branch government."

In Washington, the US state department said it was "hopeful" Snowden would be returned to the US to face charges of espionage and theft after a string of other countries said they would not accept Snowden's petition for asylum.

Speaking before the developments in Vienna, state department spokeswoman Jen Psaki rejected claims made by Snowden on Monday the US had bullied other potential hosts such as Ecuador into withdrawing their offer of asylum. "I am not sure what the basis for those claims are," she said.

The US insists it has simply impressed upon possible host countries the seriousness of the crimes that Snowden has been charged with.

Psaki also defended a decision to suspend his passport, an act which has left Snowden unable to the leave the airport transit zone and which he described as "using national identity as a weapon". The state department says such a response is normal when a US citizen attempts to flee arrest in this way.